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Single stranded DNA-binding protein (ICP8) from Herpes simplex virus-1, apo form.Mutations: K166A, E167A, C254S, C455S
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1URJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2% PEG 8,000,
100mM Hepes, pH 7.0,
40mM MgCl2,
2mM DTT,
1mM Spermine
Crystal Properties Matthews coefficient Solvent content 2.38 48.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.348 α = 90 b = 139.779 β = 111.09 c = 98.869 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 16M 2022-11-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.979300 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.75 92.42 100 0.107 0.151 0.107 0.979 7.2 2 59491
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.83 100 0.495 0.703 0.497 0.545 1.8 2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.75 92.417 59480 2972 99.97 0.181 0.1771 0.1864 0.2609 0.2669 RANDOM 38.589
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 2.207 0.49 -1.43 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.078 r_dihedral_angle_6_deg 14.728 r_dihedral_angle_2_deg 13.359 r_lrange_it 8.913 r_lrange_other 8.913 r_dihedral_angle_1_deg 6.872 r_scangle_it 5.362 r_scangle_other 5.349 r_mcangle_it 4.601 r_mcangle_other 4.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.078 r_dihedral_angle_6_deg 14.728 r_dihedral_angle_2_deg 13.359 r_lrange_it 8.913 r_lrange_other 8.913 r_dihedral_angle_1_deg 6.872 r_scangle_it 5.362 r_scangle_other 5.349 r_mcangle_it 4.601 r_mcangle_other 4.601 r_scbond_it 3.304 r_scbond_other 3.296 r_mcbond_it 2.855 r_mcbond_other 2.853 r_angle_refined_deg 1.693 r_angle_other_deg 0.518 r_nbd_refined 0.222 r_symmetry_nbd_other 0.204 r_symmetry_nbd_refined 0.188 r_nbtor_refined 0.183 r_nbd_other 0.169 r_symmetry_xyhbond_nbd_refined 0.169 r_xyhbond_nbd_refined 0.161 r_symmetry_nbtor_other 0.082 r_chiral_restr 0.067 r_symmetry_xyhbond_nbd_other 0.022 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16177 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement Aimless data scaling XDS data reduction PHASER phasing